3E49

Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel fold (bxe_c0966) from burkholderia xenovorans lb400 at 1.75 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827740.0000% 2-ethoxyethanol, 0.0500M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2244.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.495α = 69.99
b = 68.275β = 88.07
c = 83.952γ = 72.84
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-07-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97936,0.97892SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7529.65697.20.0690.0696.62.711596721.904
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.751.8960.4440.4441.72.78444

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.7529.656115965580497.240.1790.1770.218RANDOM24.44
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.31.95-0.711.19-0.31-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.629
r_dihedral_angle_4_deg13.596
r_dihedral_angle_3_deg11.904
r_scangle_it5.541
r_scbond_it4.211
r_dihedral_angle_1_deg4.019
r_mcangle_it2.417
r_angle_refined_deg1.751
r_mcbond_it1.68
r_angle_other_deg1.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.629
r_dihedral_angle_4_deg13.596
r_dihedral_angle_3_deg11.904
r_scangle_it5.541
r_scbond_it4.211
r_dihedral_angle_1_deg4.019
r_mcangle_it2.417
r_angle_refined_deg1.751
r_mcbond_it1.68
r_angle_other_deg1.039
r_mcbond_other0.321
r_symmetry_vdw_other0.268
r_nbd_refined0.215
r_nbd_other0.207
r_symmetry_vdw_refined0.197
r_nbtor_refined0.185
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.179
r_metal_ion_refined0.142
r_chiral_restr0.113
r_xyhbond_nbd_other0.108
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9355
Nucleic Acid Atoms
Solvent Atoms946
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing